Table 2.
KIR gene alleles of the centromeric LD region tagging other KIR gene alleles
| KIR tagging allele | KIR tagged allele | PPV | NPV | Haplotype frequency | D' (*) | |
|---|---|---|---|---|---|---|
| KIR2DL3 | *002 | KIR2DL1*002 | 94.30% | 99.70% | 23.90% | 0.45 |
| *001 | KIR2DL1*00302 | 94.80% | 96.60% | 35.20% | 0.45 | |
| KIR2DL2 | *003 | KIR2DS2*POS | 100.00% | 77.60% | 12.40% | 0.79 |
| *001 | KIR2DS2*POS | 100.00% | 83.30% | 18.40% | 0.79 | |
| *001 | KIR2DL5B*002 | 71.40% | 99.40% | 13.20% | 0.95 | |
| KIR2DL5B | *002 | KIR2DS2*POS | 98.20% | 78.40% | 13.40% | 0.97 |
| *002 | KIR2DL1*00401 | 78.90% | 98.10% | 10.80% | 0.82 | |
| *002 | KIR2DS3*00103 | 84.20% | 98.60% | 11.50% | 0.84 | |
| *002 | KIR2DL2*001 | 96.50% | 93.90% | 13.20% | 0.95 | |
| KIR2DS3 | *00103 | KIR2DS2*POS | 90.60% | 76.40% | 11.50% | 0.79 |
| *00103 | KIR2DL1*00401 | 69.80% | 95.90% | 8.90% | 0.77 | |
| *00103 | KIR2DL5B*002 | 90.60% | 97.50% | 11.50% | 0.84 | |
| *00103 | KIR2DL2*001 | 86.80% | 91.50% | 11.00% | 0.79 | |
| KIR2DL1 | *00401 | KIR2DS2*POS | 100.00% | 77.60% | 12.40% | 0.75 |
| *00401 | KIR2DL5B*002 | 86.50% | 96.70% | 10.80% | 0.82 | |
| *00401 | KIR2DS3*00103 | 71.20% | 95.60% | 8.90% | 0.77 | |
| *00401 | KIR2DL2*001 | 84.60% | 91.00% | 10.50% | 0.74 | |
| *00302 | KIR2DL3*001 | 94.20% | 96.90% | 35.20% | 0.45 | |
| *002 | KIR2DL3*002 | 99.00% | 98.10% | 23.90% | 0.45 | |
Only alleles of the previously defined centromeric region are displayed. Other constraints were applied: tagging must have a minimal PPV of 65%. For robustness of the estimation, only haplotypes of more than 5% were studied; haplotypes without KIR gene at another locus were not studied. (*) PPV and NPV drastically differ from D′. PPV and NPV are measures of association at the allelic level, whereas D′ is a locus-level average measure of LD. D′ stands for the pairwise standardized Hedrick’s measure of LD between multiallelic genes. Confidence intervals can be computed because frequencies were estimated by gene counting. The total number of haplotypes is 418 (~209 founders of the families). For example (2nd row), the probability of having KIR2DL1*00302 given the presence of KIR2DL3*001 is 94.8%, the probability of not having KIR2DL1*00302 given the absence of KIR2DL3*001 is 96.6%, the KIR2DL3*001–KIR2DL1*00302 haplotype frequency is 35.2%, and D′ between KIR2DL3 and KIR2DL1 is 0.45
PPV positive predictive value, the probability of the tagged KIR allele given the presence of the tagging KIR allele; NPV negative predictive value, the probability of the absence of the tagged KIR allele given the absence of the tagging KIR allele